X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=00a2ec405971542b021a483760a965ebf40be132;hb=80ac7d84002118186a11658f38abfa5c4fe3d8da;hp=51ad601f62ec5b88456f49770ed66feb8e81971c;hpb=634ec381e01c3be6f6b6bc0d833cffe3fb68fb64;p=jalview.git diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index 51ad601..00a2ec4 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -244,7 +244,7 @@ Selects all the sequences and residues in the alignment.
Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all. - +
  • Deselect All (Escape)
    Removes the current selection box (red dashed box) from the alignment window. All selected sequences, residues and @@ -312,7 +312,7 @@ or hide sequence features on this alignment.
  • Sequence - Feature Settings...
    Opens the + Feature Settings...
    Opens the Sequence Feature Settings dialog box to control the colour and display of sequence features on the alignment, and configure and retrieve features from DAS annotation @@ -427,12 +427,12 @@ If this box is selected then the sequence names displayed in the sequence label area will be aligned against the left-hand edge of the alignment display, - rather than the left-hand edge of the alignment window. + rather than the left-hand edge of the alignment window.
  • Show Hidden Markers
    When this box is selected, positions in the alignment where rows and columns are hidden will be - marked by blue arrows.
    • + marked by blue arrows.
  • Boxes
    If this is selected the background of a residue will be coloured using the selected background colour. Useful if used in @@ -461,7 +461,6 @@ symbols will be rendered as a '.', highlighting mutations in highly conserved alignments.
    • - @@ -541,44 +540,26 @@ viewer window.
    -
  • Calculate Tree
    Functions - for calculating trees on the alignment or the currently - selected region. See calculating - trees. - - Note: Since Version 2.8.1, a number of - additional similarity measures for tree calculation are - provided in this menu.
    • -
  • Pairwise Alignments
    Applies - Smith and Waterman algorithm to selected sequences. See pairwise - alignments. +
  • Calculate Tree or PCA ...
    Opens the + calculations dialog for + for calculating trees or + principle component analysis + plots on the alignment or the currently selected + region.
    • -
  • Principal Component Analysis
    Shows - a spatial clustering of the sequences based on similarity - scores calculated with the alignment. See Principal - Component Analysis. -
    • -
  • Extract Scores ... (optional)
    This - option is only visible if Jalview detects one or more - white-space separated values in the description line of the - alignment sequences.
    When selected, these numbers are - parsed into sequence associated annotation which can then be - used to sort the alignment via the Sort by→Score menu. -
    • -
  • Autocalculate Consensus
    For +
  • Pairwise Alignments
    Applies + Smith and Waterman algorithm to selected sequences. See pairwise + alignments. +
    • +
  • Extract Scores ... (optional)
    This + option is only visible if Jalview detects one or more + white-space separated values in the description line of the + alignment sequences.
    When selected, these numbers are + parsed into sequence associated annotation which can then be + used to sort the alignment via the Sort by→Score menu. +
    • +
  • Autocalculate Consensus
    For large alignments it can be useful to deselect "Autocalculate Consensus" when editing. This prevents the sometimes lengthy calculations performed after @@ -614,7 +595,7 @@ in Jalview 2.8.1
  • 'Standard Databases' will check sequences against - the EBI databases plus any active DAS sequence sources<
    • + the EBI databases plus any active DAS sequence sources Other sub-menus allow you to pick a specific source to query - sources are listed alphabetically according to their nickname.